Okay, that makes sense. I'll switch over to making sure each tool
dependency is in a separate repository with version names. It was just one
repo which we were updating a lot that ended up with multiple versions so
it's an easy thing to do.

Thanks,
Aaron
On Wed, Nov 4, 2015 at 12:18 PM, Martin Čech <mar...@bx.psu.edu> wrote:
> Hi Aaron,
>
> I think Galaxy will always install the latest revision of the selected
> installable revision. Our approach was that tool dependencies have
> versioned repositories (with versions in the names) so that it cannot
> happen that abyss 2.0 would be in the package_abyss_1_9_0 repo. With this
> in place you shouldn't care about the actual revision because it will
> always install correct version of the tool.
>
> Carefuly following this fragile approach you should be able to achieve
> what you want. :/
>
> Thank you.
>
> M.
>
>
>
> On Wed, Nov 4, 2015 at 1:09 PM Aaron Petkau <aaron.pet...@gmail.com>
> wrote:
>
>> Thanks Martin, that helps me out. However, the issue I'm running into is
>> that it seems like specific revisions in my repository suite definition are
>> being ignored and it's only using the latest one.
>>
>> I think what may be happening is as follows.
>>
>> In my repository suite I have a dependency like:
>>
>> <repository changeset_revision="0" name="package_x" owner="devteam"
>> toolshed="http://toolshed.g2.bx.psu.edu&quot; />
>>
>> Now, "package_x" defines dependencies for tools in a
>> "tool_dependencies.xml" file. And it has been updated to a newer revision,
>> "1".
>>
>> Looking through the toolshed, it looks like revision "0" for "package_x"
>> isn't being set as an installable revision. So, when installing my older
>> repository dependency suite, it's ignoring revision "0" and just installing
>> revision "1".
>>
>> Is there any way to force it to install revision "0" of package_x?
>> Should I never be updating the repositories for tool dependencies?
>>
>> This was all being tested out with toolshed tag "v15.05.1".
>>
>> Thanks,
>>
>> Aaron
>>
>>
>>
>> On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>>
>>> Hi Aaron,
>>>
>>> we touched this recently here:
>>> https://github.com/galaxyproject/tools-devteam/pull/267
>>>
>>> I believe that if you specify the repository_dependencies.xml of your
>>> suite in the following way:
>>>
>>> <repositories>
>>> <repository changeset_revision="f2ab5b44870d"
>>> name="fasta_clipping_histogram" owner="devteam" toolshed="
>>> http://toolshed.g2.bx.psu.edu&quot; />
>>>
>>> you will pin the exact revision of the tool (fasta_clipping_histogram
>>> here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
>>> suite_fastx_toolkit_0_0_9 repositories which will install the requested
>>> versions of the tools.
>>>
>>> M.
>>>
>>> On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau <aaron.pet...@gmail.com>
>>> wrote:
>>>
>>>> Okay, thanks Dave. That makes sense. Moving forward I'll just make a
>>>> new suite with a version number in the name.
>>>>
>>>> Another question, does the same apply for tool dependency definitions?
>>>> I've upgraded a suite of tools + dependency definitions, and now even if I
>>>> make a new repository suite (to allow installing of my old set of tools,
>>>> revision 0 in my example) it's installing the newer commit in one tool
>>>> dependency definition repository.
>>>>
>>>> Thanks,
>>>>
>>>> Aaron
>>>>
>>>> On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <d...@bx.psu.edu> wrote:
>>>>
>>>>> Aaron,
>>>>>
>>>>> Repository suite definitions are designed to only allow the latest
>>>>> revision to be installable. My recommendation in this case would be to
>>>>> define two separate suites tagged in some descriptive way, so the
>>>>> individual use cases would have their appropriate suites.
>>>>>
>>>>> -
>>>>> Dave Bouvier
>>>>> http://galaxyproject.org
>>>>> http://usegalaxy.org
>>>>>
>>>>>
>>>>> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I'm running into some issues with maintaining multiple installable
>>>>>> revisions for a repository suite and I'm not sure if there's something
>>>>>> I've missed.
>>>>>>
>>>>>> I have a local toolshed where I'm maintaining my tools, and I have a
>>>>>> repository suite definition, defining a number of dependencies. So,
>>>>>> I have:
>>>>>>
>>>>>> suite_X (mercurial revision 0):
>>>>>> Dependency A
>>>>>> Dependency B
>>>>>>
>>>>>> I updated "suite_X" and changed the dependencies:
>>>>>>
>>>>>> suite_X (mercurial revision 1):
>>>>>> Dependency A
>>>>>> Dependency B
>>>>>> Dependency C
>>>>>>
>>>>>> I would like to have both mercurial revision 0 and 1 installable in
>>>>>> Galaxy, but only revision 1 (the latest) is showing up as installable.
>>>>>> I found documentation at
>>>>>> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
>>>>>> only cover a repository containing a single tool, not a suite of
>>>>>> tools.
>>>>>>
>>>>>> Is there something I'm doing wrong or some setting I have to change
>>>>>> here? My toolshed is running with Galaxy tag "v15.07".
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Aaron
>>>>>>
>>>>>>
>>>>>> ___________________________________________________________
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>>>>>>
>>>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
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>>>
>>>
>>